


A Mother's Justice

by Brony4Ever1992



Category: Neon Genesis Evangelion
Genre: Action/Adventure, Drama, F/M
Language: English
Status: Completed
Published: 2012-02-10
Updated: 2012-02-18
Packaged: 2017-10-30 22:10:12
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 6
Words: 12,971
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/336684
Author URL: https://archiveofourown.org/users/Brony4Ever1992/pseuds/Brony4Ever1992
Summary: <blockquote class="userstuff">
              <p>When Shinji is targeted and his life put in danger Misato vows to track down those responsible and make them pay. This pits her against a bloody terrorist organization that puts her on the top of it's hit list.</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

> A/N: Here is my third story and first drama "A Mother's Justice".

Thanks to my pre-readers Young Boch and gunman with a special thanks the latter for helping me fix this chapter before I posted it..

Disclaimer: I do not own Evangelion it is the property of Gainax.

"Ahhhhh!" the loud cheer that could only mean one thing, Misato Katsuragi had finished another can of Yebisu beer which was her fourth that day.

It was noon at the Katsuragi/Ikari/Soryu residence and Misato had been drinking since she woke up an hour ago after the sun had found her and woken her from her blissful slumber.

It was Saturday and since there were no synch tests the kids had the day off. Asuka had left earlier to go to the mall with Hikari and Rei was doing what ever she did on her down time. Shinji was watching TV with Pen-Pen enjoying not having Asuka ordering him around. (But secretly wishing that she was there.)

The came a call from the kitchen "Hey Shinji! I'm starved can you cook something please? I've been working so hard at NERV."

Shinji rolled his eyes, being more mature than the guardian who was twice his age was very exhausting at times. "There are left overs in the fridge", came the response from the Third child.

Misato went over to the refrigerator and saw a plate of left over sushi from a few nights ago when Shinji was too tired to cook. (And there was thankfully no instant ramen so Misato couldn't whip up a batch of the biological waste she called "food".)

Then Misato asked "Hey Shinji, I found left over sushi you want some?"

Before he could respond, Shinji's stomach growled quickly betraying any resistance the boy could put up.

Shinji went over to the table leaving Pen-Pen to continue watching TV, Misato severed up the sushi and was about to eat when nature called. "Oh! Save me me some, I'll be back in a sec." said the female Major before heading off to the bathroom.

After relieving herself Misato returned to see Shinji at the table holding his stomach in pain as a half finished roll sat on his plate.

"What's wrong?" she asked in a concerned voice.

Shinji looked up at her and said "The sushi is bad", then looking away added "I'm sorry", in typical-'Shinji' fashion.

Misato responded with a calming smile and said "It must be food poisoning just lie down for now."

As Shinji went to his room Misato through out the sushi and after searching around found her precious curry powder in the cupboard. Mixing it with water a whole bunch of other odd ingredients she happened to find, she stuck it in the microwave and then hit "Power" before grabbing her fifth beer before and eventually joining Pen-Pen on the couch.

Thirty minutes later the phone rang, Misato was going to ask Shinji to get it before remembering his illness. Her next step was to call Asuka but after remembering she was gone looked to Pen-Pen before going to answer the phone saying "They won't understand penguin".

Misato picked up the phone and answered. "Hey Kat-" she started to say only to get preempted

(How did you like the sushi?) Said an unknown voice that was obviously scrambled and sounded sadistic.

"I threw it out a half hour ago. I think it had gone bad." responded Misato who was now very confused by the call.

(Wait! Are you Misato Katsuragi?) said the voice now more concerned than anything.

"Yes", Misato said before adding "Who is this and how did you get this number?" she demanded in the strict voice she used only during battles with the Angels.

The voice didn't answer right away as the owner started talking to himself and swearing. Then came the one statement that made Misato's heart stop.

(How are they not dead?) The voice said

"What the hell do you mean 'how are they not dead !'" yelled Misato to the unknown caller.

The only response she got was (Crap!) as the voice released the mistake it made and hung up.

"That was really weird" said Misato in her normal tone, before returning to the living room. "I wonder what they meant by..." , however, she paused halfway to the couch, dropping her beer as a sudden realization caught up to her. "Shinji" she said her eyes now as wide as saucers.

Misato ran to Shinji's room throwing the door open and seeing her ward in terrible pain as he hugged his stomach tightly.

"Dammit!" Misato yelled. Quickly grabbing Shinji, she lifted him up in her arms, she quickly put on her jacket with her NERV ID in it. She put her shoes and on ran out the apartment down the stairs and to her car all while carrying Shinji in her arms. Misato put Shinji in the passenger seat of her blue Renault Alpine before driving off like a bat out of hell, this time with a reason, before heading straight to NERV.

It was five hours later, and Misato paced in the waiting room at the NERV infirmary like someone waiting for the birth of a child. Dr. Akagi had been preforming all kinds of tests in those five hours and still no news. Word had spread through out NERV and everyone from Lieutenant Hyuga to Kaji and even Sub-Commander Fuyutsuki had come by to console her and ask on Shinji's progress. Commander Ikari had not shown up.

Finally Dr. Akagi walked into the waiting room with assistant Maya by her side, which was to be expected.

"Rits" Misato began "Is he...I mean will he...Is he going to be...", but she couldn't find the words.

"Misato" began Akagi, the Head of Project E was at a lose for word which for Ritsuko Akagi was foreign to her "Shinji has been poisoned, I don't know what type of poison though".

"I threw the sushi out but should still be in the trash." said an anxious Misato

"Good, Hyuga will drive you home tonight and pick up the poison, you need to rest. " said the doctor before adding "The MAGI will analyze the sushi, we will find out what poison it is and create an antidote for Shinji."

"Okay Rits, I'll see you tomorrow" said the worried Misato Before she left Misato turned back to the faux-blond "Rits, how is Shinji?"

"He has stabilized but... but nothing is sure. I can't tell if anything permanent will come of this. Shinji has had his stomach pumped and is currently resting. Only time will tell."

"This was deliberate" said Misato in anger voice "Someone was trying to kill him."

After saying this Misato bowed and thanked Ritsuko before leaving NERV.

Meanwhile in the dark abyss known as the office of Commander Ikari...

"Professor where have you been?" has the Commander sitting at his desk, signature pose already in place as he knew the answer to his own question.

"I was visiting your son, he was poisoned by a would-be assassin." replied Kozo. After returning from visiting Misato to check in on Shinji.

"Do you think it was SEELE?" asked Gendo

"No" replied the gray haired man "Keel and the rest of the committee have no reason to kill any pilot. And besides, if it was SEELE they would have targeted Rei."

"Who ever is responsible must be hell responsible for this." said Gendo sternly before getting up to go home. As he passed Fuyutsuki he said something that made the old professor smile "Nobody messes with my son."

As Hyuga drove Misato home she thought about the last 24 hours for clues. The kids had gone to school and she had gone to work, nothing unusual. There were the newly weds Yoshi and Ai Nohara who were always lovey-dove, the old married couple who argued like it and who Misato compared to Asuka and Shinji, Ms. Yoshida the elderly lady who could still remember the Japanese surrender to the U.S. on the USS Missouri September 2,1945 that ended WWII, even the Shinzo the delivery boy who had dropped off the belongings of one Asuka Langley Soryu when she arrived but nothing was odd or out of place.

"That's it then" decided Misato as she sat in the passenger seat with tears in her eyes "I swear... whoever is responsible for this will pay!"


	2. Chapter 2

**Summary for the Chapter:**

> Misato begins her quest for revenge.

**Notes for the Chapter:**

> A/N: Here begins chapter two.

Disclaimer: I do not own Evangelion it belongs to Gainax

"Dammit" said a frustrated Misato Katsuragi as she rode the elevator back to her apartment.

"No clues, nothing to hint at tried to kill Shinji.", she had racked her brain for any evidence to of who might have poisoned the sushi that Shinji ate but found nothing and was mentally exhausted as she and Hyuga entered her residence.

"Hello Pen-Pen, I'm home." said Misato who needed to unwind but instead of the pet penguin someone else greeted the Major and her Lieutenant with a different response.

"There you are! Where have you been and where is Shinji? I am starving so that idiot better get diner started right away and if you even try to suggest cooking I swear I will call Child Protective Services!" an angry redhead shouted an angry redhead as she rushed into the hallway.

Misato looked over and cringed, in her worry over Shinji she had forgotten about Asuka. She didn't mean to but she was worried over Shinji. It wasn't like Asuka needed looking she could take care of herself but with at least one assassin if not more on the loose she needed to keep an eye on the girl. Add to the fact the assassin might have gotten into the apartment meant Misato couldn't trust Section 2. The purple-haired woman motioned to Hyuga where the sushi was and the addressed her ward with in a grim and solemn tone.

"Asuka.", Misato began not knowing how to break the news so she just came straight out with it "Shinji is in the NERV infirmary, someone poisoned the leftover sushi and I am certain they were trying to kill all three of us."

Worry replaced anger on the face of the fiery redhead.

"How...how is baka doing?" asked the Second Child trying to keep her usual facade but the concern on her face betrayed her.

"He has stabilized but nothing is sure now. Ritsuko is looking after him and I will lead the investigation into exactly what happened." replied the Major who only nodded as Hyuga left with the tainted sushi.

Asuka went to over to the refrigerator but was stopped by Misato who told her "We don't know if anything else is poison so all food is off limits Asuka."

Asuka didn't protest, the news about Shinji had ruined her appetite so she went to her room while Misato gathered the tainted sushi from the trash.

That night neither female slept well.

 

The next day was Sunday and the two remaining residence of the Katsuragi/Ikari/Soryu apartment were eating take out with the refrigerator on quarantine. Misato was at the table while Asuka sat on the couch watching TV with Pen-Pen, the similarity was so eerie to the previous day Misato couldn't look over in that direction. As Asuka got up to throw out her empty soda can into the recycling when the doorbell rang, she went to answer it with out protest and was not pleased by the visitor.

"What the hell are you doing here Wondergirl?" Asuka snapped

The fact that Rei Ayanami, the blue-haired, red eyed First Child was at the door and wanted to come in was the last thing Asuka wanted right now.

"Dr. Akagi sent me over here to give an update on Pilot Ikari so may I please enter Pilot Soryu?", said the albino in her cool manner.

"Fine.", huffed Asuka, as Rei entered Asuka called to the kitchen "Misato, Wondergirl is here!"

Misato entered the hallway and in with an obviously forced smile said "Hello Rei what brings you here, don't you have synch tests?"

"I finished and was sent here to give an update on Pilot Ikari." stated the First

Misato's eyes shot open "How is he? Will he be okay? Please tell me!" In a frantic voice.

Rei responded as conditioned, with matter of fact and straight to the point.

"Pilot Ikari has not gotten any better or worse since yesterday ma'am." after she bowed and began to leave the apartment.

"Rei," began Misato "Are you okay?" despite her usual demeanor Misato still picked up something wasn't right with Rei Ayanami.

Rei was confused, she was worried for Shinji, an emotion Commander Ikari told her was useless and one she have never experience before, because of this she had no idea how to handle the situation so to hind her budding emotions Rei answered as normal as was possible for her without turning around.

"I am all right Major, Shin-Pilot Ikari's ailment will not interfere with my duties." came the answer from the First.

As Rei reached the door, Misato stopped her again because of a hunch the three of them were not the only targets.

"Rei, have you received any suspicious gifts lately, maybe food?"

After a moment of thinking Rei turned around to face the two whose apartment she was in "Yes, I was offered chofu by a strange man this past Wednesday."

This was a new and excellent development, the kind Misato needed.

"Rei can you remember this man,what did he look like?"

"He was 5 ft. 6 in. (168 centimeters) and 165 lbs. (75 kilograms) average for a Japanese man. He wore a brown trench coat and at first I thought he was one of the 'perverts' that Commander Ikari warned me about who usually expose themselves or abduct children but this was not the case."

Asuka mumbled something about Rei being abducted while the First Child continued .

"He also had on a brown fedora hat and plastic novelty glasses that were black in color and with a bulbous plastic nose attached." This made Misato think about Groucho Marx and made almost ask Rei if the guy had a cigar with him, bushy eyebrows and a this mustache but she didn't and Rei went on with her description still.

"He offered me chofu and I accepted not wanting to be rude but when I arrived at NERV and told Commander Ikari he made me throw them away." finished Rei

Now Asuka spoke up , "Think Wondergirl was there anything odd about this guy?"

After thinking for a moment Rei responded "Yes, part of his right ear was missing."

(A/N: The failed assassin is not Mick Foley)

This was great for Misato but the description Rei gave sounded familiar to all three ladies it was creepy. The problem was none of them could pinpoint where the similarity came from.

"Thanks Rei your information is very helpful", said Misato "Now lets go Asuka. I'm not letting you out of my sight, both of you are sticking with me today."

"But Misato I already have plans with Hikari.", replied Asuka but Misato wouldn't hear it and soon both girls were in Major's Renault Alpine.

 

When the trio got to NERV they went directly to Dr. Akagi's office and were greeted by the fake blonde and her faithful assistant Lieutenant Maya Ibuki.

"Why are you three here?" asked the doctor.

"I got a break, Rei was also offered food by someone and I think it might be the same person. Lucky for us she gave a great description.", Misato responded

"Given food?", Akagi asked as she could not remember replacing a clone because of poisoning.

"I did not par take on the orders of Commander Ikari.", responded said clone

Akagi got the picture now and brought the Major and pilots to the MAGI "It has been testing all night,what ever was used is not a normal poison but we can still determine what is with 99.9% accuracy and a margin of error of .000000000000001%."

As the MAGI tested the sushi Lieutenant Hyuga brought back all was quiet in the control room with only Misato, Rei, Asuka, Dr. Akagi, Maya present along with Hyuga and Aoba at their stations.

As the MAGI was testing Akagi's eyes lit up and she turned over to her old college friend.

"Misato, Thursday I found a box of chocolates at my door with no name, you think it might be same person behind these?"

"Rei on Wednesday, Rits on Thursday and the three of us on Friday." Misato mused "No doubt it is the same person and from the targets these attacks definitely has to do with NERV."

"Maya!" started Akagi as she threw her keys at the Bridge Bunny "These are my keys to my apartment the chocolates are in my fridge." causing Maya to blush.

"Rei what exactly did you do with the chofu?" she asked

"I threw into my trash receptacle but since trash is not picked up until Tuesday it should still be there." Rei answered

"Right. Rei go with Lieutenant Ibuki she'll go to your apartment and you just need to need to grab the chofu.", ordered the Director of operations.

It took about thirty minutes to leave NERV, go to both apartments, the duo returned just as the MAGI gave the results of the tests.

"You are not going to believe this!", began a surprised Akagi but the substance used to poison the sushi was Brugmansia, also know as Angel's Trumpet, which can be deadly if ingested. We'll create an antidote immediately. "

"That sick bastard is messing with us!" yelled an irate Katsuragi

Akagi tested one chocolate and chofu, and was more surprised by the results of these tests.

"The substance used to poison these were potassium arsenic." said the doctor "How odd that he uses such a potent poison as that at first then switch to a plant."

"Either we are dealing with a botanist or the assassin was not acting alone." said Misato

That night Rei stayed at Misato's flat sleeping in Shinji's room so she would not be vulnerable to an assassin well alone. Not one of the three got much sleep.

**Notes for the Chapter:**

> A/N: Chapter 2 was longer then I thought. A few things, first somebody might want to double check my math on the height and weight translation, I am American and thus am unfamiliar with the metric system. Chofu is a popular Japanese is a pastry. Groucho Marx was on the famous Marx brothers, comedians back in the 1930s and 1940s and the appearance of the man who offered Rei the poison mirrored Groucho with out the hat. Mick Foley is professional wrestler who besides his name has wrestled as Dude Love, Mankind and most famously Cactus Jack. It was as the last persona that in 1992 Foley wrestled Vader (real name Leon White) in Munich, Germany and during that match Foley was slammed on the rope which is a thin covering over steel and had part of his ear torn off which helped to cement Foley's reputation as a hardcore icon. As for Gendo warning Rei about perverts I know that is ironic. Brugmansia is real and with it's other name I thought it appropriate. Arsenic is a deadly an commonly used poison. An additional warning that Windows system tools is also malware.
> 
> I hope you check out my Evangelion demotivational poster video on YouTube, my name their I EssexAggiegrad2011 and my account on where my name is Thehumanhistorybook.
> 
> I also encourage you to read my fanfic "Pathetic" if you haven't.
> 
> Starting in July I began a crossover of Evangelion with Strike Witches (which I'll post here soon) and to have fun I added a list of random letters with the title of that crossover hidden with in and I will dedicate the first chapter of the crossover to the first person who can send me a personal message with the correct title. It's on my profile if you want to try. I feel I should warn you my personal messenger and email have been disabling themselves so I might not get your response and it's not on purpose if you're right but I don't acknowledge it it is an accident and I'm sorry.
> 
> Next time a revelation from an unlikely source blows the case wide open. Thanks and to quote Mick Foley's persona of Mankind: Have a nice day. Don't forget to review!


	3. Chapter 3

**Summary for the Chapter:**

> Mistao continues her quest as the identity of the would be assassin is revealed.

Thanks to my pre-reader gunman.

Disclaimer: I do not own Evangelion it is the property of Gainax

Hikari Horaki was patiently waiting at the entrance of the middle school. It was Monday morning and she was waiting for her friend, Asuka, to arrive.

"If she's not here soon then she and Shinji will be late." said the class rep who, having not talked to Asuka since Saturday, had no idea of Shinji's condition.

Only thirty seconds after finishing that statement Hikari saw Asuka and another person running to the school. At first she was re-leaved but that changed to confusion once she saw Asuka was not accompanied by Shinji as usual, but rather by Rei, the one person Asuka seemed to despise more than anyone else.

"Crap! Were not late, are we? We would have gotten her soon but Wondergirl was took her sweet time in getting ready this morning." said the out of breath German

"No" began Hikari "but where is Shinji?" the pigtailed student asked, puzzled but what she saw before her eyes.

Just as Asuka was about to answer, the bell rang.

"Schiest! We're gonna be late!" she said. Hikari was now too worried about running her perfect attendance record and forgot about their conversation.

 

A loud screech of tires could be heard for an entire city block, signaling Misato Katsuragi had arrived at her destination. The place were she had to rush of to was the sushi restaurant five streets over from the apartment. More importantly it was where the sushi had come from that had been poison, and while Misato knew the chance of finding answers from this place was slim she would not leave any stone unturned in her mission. She entered the place, it was small restaurant with powder blue wall that had Shinto scrolls nailed to them. Thankful that the restaurant was now closed, Misato made her way past the two dozen empty tables and up to the counter.

Asuka couldn't pay attention. Not like she really did anyway because for someone with a college degree it was boring to listen to the teacher drone on about Second Impact.

"And that's why I live with my nephew." droned the senile old man relating for the millionth time the story of how his two floor, $15 million yen home that he won in the divorce was flooded and ruined.

"Mein Gott! It's been fifteen years! Just get over it already!" though the redheaded spitfire, but her mind was else where.

"Shinji..." she muttered under her breath. Unlike most kids Asuka wasn't on her laptop on what were usually "inappropriate" websites. She had gotten messages from a concerned Hikari as well as from Toji and Kensuke asking where Shinji was. The latter pair brought her mood down even more.

"Why I am worried about that idiot? " Asuka thought angrily to herself " Why would I care about him? After all he is just a perverted, stupid, housebroken male and there is no way I could care about him more than that... or could I?" Asuka felt her mind wander back to the battle against the eighth Angel, when Shinji saved her from the volcano and the kiss they shared, "Stop it! I won't let anyone close because they'll just leave me like mama!" she tried to hide her pain but when she might lose him regardless, just like she lost her mother, she shut her laptop and rested her head on it with her face down to hide her emotions.

 

Meanwhile, Rei was in the same boat, she stared out the window not paying attention to the teacher. She had also received messages from the two non-pilots and now former Fourth Child with the same questions they had asked Asuka but since Rei never used the school's messenger she didn't look at these which was good or she would have joined Asuka.

"Why does Pilot Ikari's situation bother me so?" thought the blue-haired pilot. "Commander Ikari told me emotions are useless and not to feel." This caused Rei to feel a tug at her heart string because the Commander had always the closest person to , if you can call it, that but then Shinji came along and his genuine caring threw Rei for a loop. "The Commander has always been there but with then Shinji-"

Rei stopped, she just used Shinji's first name. This confused Rei "Is my loyalty to the Commander or is it to myself as Shinji has encouraged me to think? I need to do more research on-no, I will visit Shinji after school today. Commander Ikari will be second priority. "

Class lasted thirty more minutes before the bell announcing lunch. The bored kids ran out of the classroom like a pack wild wolves on the hunt.

"So Asuka, where do you where do you want to eat lunch?" asked Hikari causing Asuka to lift up her head from the closed laptop.

"The maple outside is fine." answered Asuka before adding "Let's go doll, time for lunch!" which was followed by Rei snapping out of her trans and walk over to the two.

"You're inviting Rei?" asked Hikari, once more confused by what was happening.

"Misato's ordered. I have to stick close to her." replied the German still adverting her eyes so Hikari couldn't see she her worry and sorrow.

"Hold it!" the girls were interrupted by a loud voice belonging to ex-pilot Toji Suzuhara. "What did you to Shinji you demon!" he said with finger pointed right at Asuka.

'I didn't do anything to the idiot!" Asuka retorted not wanting to go at it with Toji but she couldn't look as if something was wrong so she acted as to be expected from her.

"Then why is he not here?" chimed in Kensuke

Both Asuka and Rei turned their heads and Toji knew what it meant.

"NERV?" he asked, his hand subconsciously rubbing his prosthetic leg.

"We will inform you as best we can at lunch." said Rei, and with that the teens were off.

 

"What the hell?" yelled Hideaki Mitsumeki as Misato held him against the wall of the restaurant. Mitsumeki was the manager of the restaurant, 38, he had worked there since he was fifteen and had been manger for three years now."

"I want answers NOW!" yelled the angry NERV major "Is there any chance somebody at the restaurant could have tampered with the food?"

"What do you mean?" asked Hideaki more scared then confused

"Sushi from this place almost killed one of my wards!" screamed Katsuragi

"My god! I am so sorry but all food paces by me, and I swear it was fine!" said Hideaki scared

Misato dropped him, he she had know Hideaki since she came to Tokyo-3. She was convinced he had no connection to the incident. Misato bowed and apologized before leaving.

"Damn" the violet-haired woman cursed drove away in her Alpine, "I should check in on Shinji." Misato fished around for her id but remembering she left it home went back to the apartment.

 

"That's awful!" proclaimed Hikari, Asuka and Rei had finished telling them the story of what happened while sharing their friends food, as theirs was still on quarantine.

"Will he be okay?" asked Kensuke

"Doctor Akagi his monitoring him, so he is in capable hands." said Rei while ignoring Asuka's sarcastic remarks about the faux-blonde.

"Hey, I just thought of something." said Toji

"It's a miracle!" exclaimed Asuka cutting the Osakan off.

"Shut up! Anyway the description Rei gave, don't that sound like that maintenance guy yous got?"

Asuka's eyes widened in shock. "Holy crap! Toji Suzuhara that is the smartest thing you have ever said!" she cried having for a split second let her emotions get the best of her.

"Mr. Kiamora does fit the description of the person perfectly." stated Rei

"Who?" asked a dumbfounded Kensuke

"We met him after we visited Asuka and Shinji" said Hikari

"It was when the dressed alike" added Toji with a snicker

"Shut up we had to battle do everything together to defeat the seventh Angel!" Asuka yelled in defense before adding "Takumi Kiamora is the head of maintenance at our apartment. Why would he go after Shinji, I wonder?"

Maybe someone got to him, offered him money or power?" asked Kensuke

"Stop talking crazy, Kensuke!" snapped Hikari

"A little late for that, Hikari" declared Asuka

"Pilot Soryu, call Major Katsuragi and inform her of this development." said Ayanami

Asuka took out her cellphone and called Misato but got no answer and instead left a message on the answering machine. Once Asuka was done, the bell rang and the kids went back to class, more rejuvenated with this new break.

 

Misato had arrived at the apartment and was walking to her flat. As she approached it she noticed the door had been kicked in.

"Shit." Misato hissed, drawing her gun and bursting in. The apartment was empty but trashed. The furniture was flipped over and everything was scattered on the floor. As Misato got to the living room she saw a message on the wall in red.

'WATCH YOUR STEP BITCH OR YOUR NEXT!'

This only angered Misato more as she went to every room except one and found them also trashed. The last room was Shinji's.

"Please God let this room be okay" she and before she entered, only to find it also ruined.

The pillow and futon were torn to shreds, the dresser draws were yanked out, Shinji's SDAT was smashed and his cello was in splinters. Upon seeing this Misato flew into a rage letting out a scream that could be heard throughout the apartment. She was so angry the phrase 'pissed of ' was downplaying her emotions.

As Misato stormed into the living room she found something moving under a blanket. Misato went over to the mass and drawing her gun but the moving object the blanket just turned out to be a frightened Pen-Pen.

"It's okay" she said as she soothed her oldest roommate after which she picked up the answering machine off the floor and plugged it in to find two messages: The first was Ritsuko saying nothing else in the refrigerator was tainted and the other was Asuka:

(Misato, we figured it out it! The guy who tried to kill baka was Takumi Kiamora!")

Misato was stunned, it seemed so obvious now but that didn't matter because she knew Asuka had to be right on this.

Misato grabbed her ID and run to the car calling Commander Ikari as she moved.

"Commander? It's Major Katsuragi, I know who poisoned Shinji. His name is Takumi Kiamora and he works at my apartment. But he has the day off so I am going to his apartment!"

"Good Major, I'll have him brought in for questioning." replied Gendo who hung up

"So we have break finally." said Fuyutsuki

"Yes" replied the bearded commander "I have hurt Shinji so much, but I'll be damned if somebody else hurts him too."

Misato got into her car to apprehend the suspect, not wanting to give the man a chance to run but she failed to notice the white van across from the apartment building.

"She didn't listen to us." said the driver

"Does that mean we get to kill her now?" asked the passenger anxiously

"Yes", said the driver

"Awesome!" exclaimed the passenger as he cheered his new assignment.

**Notes for the Chapter:**

> A/N: That was long chapter and it took me 2 hours to write. The story is almost over and things are picking up as the terrorist group behind this is revealed in the next chapter. Sorry if I screwed up on Rei and the seeming grammar errors with Toji are not, I was trying to capture his accent. Takumi is a reference to NANA. Don't forget to review


	4. Chapter 4

**Summary for the Chapter:**

> The identity of the terrorist group is revealed and later Misato is attacked.

**Notes for the Chapter:**

> A/N: Happy Birthday to Shinji Ikari. Thanks to everyone who has supported me so far. This chapter will focus mostly on the terrorist group behind the attempted murder of Shinji so bear with me. Also, I want to state now I have no ill will against anybody's religion, country or ethnic group so if anyone that does happen I am sorry but I don't mean to as I am very liberal and respectful of everyone's nationality and beliefs as well as the right to self-determination so I don't mean any content as prejudice. Thanks, I hope I don't anger anyone. Sorry for all the talking and parenthesis but it is necessary

Thanks to my pre-reader gunman

Disclaimer: I don't Evangelion it is the property of Gainax

The interrogation room at NERV was your stereotypical interrogation room you might see in a movie. The room was black except a pendant lamp in the center of the ceiling. The lamp shown down on the only furniture in the room, a wood table with two wood chairs on opposite sides.

"This is crap" snorted Takumi Kiamora.

The prime suspect in the poisoning of Shinji Ikari sat in the chair opposite the door. He was mercifully picked up by Section 2 before Misato could get to his apartment so he wasn't in a body bag. Yet.

The Major sat opposite Kiamora because the Commander allowed her to question him against the advice of Sub-Commander Fuyutsuki, Doctor Akagi and even Kaji.

"Why?" asked the Major simply as she looked right at Kiamora with dead pan eyes. "Why did you try to kill Shinji?" To which she got no response.

After a few moments of silence Misato spoke again.

"Tell me now dammit!" she yelled as she slammed her fist on the table and this time got a response.

"You are the reason. The boy and girl were also targets as per the leader's orders but you were my main target, the one I really wanted dead." Kiamora said with absolute contempt in his voice.

"Why and who is this leader of yours?" Misato spat back

"When I couldn't pass my exams and flunked out of high school I moved around for a while before I got a job with the Japanese Maritime Self-Defense Forces as a repairman on the battleship Dejima fixing equipment" he began.

Misato knew she heard of the ship before and then remembered, it was in 2007 and she was in college when the boiler on the Dejima explodedwhile the ship was in port, sinking it.

Seeing the realization on her face Kiamora continued ,"I was in the boiler room when it happened and that is how I lost part of my ear from the shrapnel and I was lucky I was alive. How do I get treated? I was thrown out by the JMSDF and within weeks I'm homeless! The only friend I had for three years was alcohol and so I drank and drank to the point of near death. In 2010 I got sober and try to get my life on track, and in 2012 I got a job with NERV. It was great and I loved it there but then I got fired so I started to drink heavily again after two years sober and got a job working as a maintenance worker in that run down crap hole you call an apartment! Your moving in was a coincidence."

Misato memory sparked as she heard that, she had read a personnel file on Kiamora and he was fired for stealing computer equipment which he then resold

Kiamora kept going smugly "I was treated like dirt by everyone there as I did for them the most degrading jobs possible. I was at the end of my rope when followers of the leader contacted me. They help me get sober, got me my own apartment and it was them who taught me how evil NERV for slaying the holy Angels. When this mission came I gladly took it."

Misato was starting to see a pattern here. This guy had fallen on hard times, one after another, with bad experiences with both the army and NERV, he was vulnerable and this terrorist group used that to brainwash him into joining them.

"Who is this leader and why does he want NERV destroyed?" asked an anxious Misato who wanted more than anything to get revenge for Shinji but was instead met with silence.

"Talk to me!" yelled the almost frantic Major but instead of giving more information Kiamora made the greatest mistake of his life.

"That little bastard deserved to die."

Misato flew into a rage upon hearing that. She grabbed the chair and she was sitting in and threw it at Kiamora trying to take his head off but Kiamora ducked and the chair hit the wall exploding into broken pieces. Misato then used the opportunity given by Kiamora ducking down to jump over the table after delivering a roundhouse to his head punching Kiamora in the face non stop until eight Section 2 agents pulled Misato off and removed her from the room as she screamed death threats to the battered man.

With Misato gone Kiamora looked up to see Gendo and a quartet of Section 2 agents around him and spat blood at Gendo's feet in between gasps of breaths.

"I'm not giving you shit."

Gendo didn't flinch and in a calm way looked to the head of Section 2 and simply ordered "torture him" which Section 2 followed up on.

 

An hour later Misato, Doctor Akagi and Kaji found themselves in the NERV debriefing room (the one from episode 9) as Commander Ikari stood at the front and Fuyutsuki stood in the back manning the slide projector.

"We are here because thanks to 'intensive interrogation' tactics we have received highly valuable information we need on the people behind this." began Commander Ikari who nodded causing Fuyutsuki to change slides. The first slide shown was of a man in his early thirties. He had hazel eyes and black hair. He stood 6 ft. 2 inches. "This is Junichiro Aizen the leader of the terrorist group responsible for the current status of the Third Child."

"So that's the head bastard then." said an angry Misato hissed

"Correct" said Commander Ikari who continued "Aizen was born in Ogaki, Gifu prefecture in 1984 as the son of a housewife and a father who was an agitator for the far-right. At fifteen he joined the xenophobic and nationalist Japan First organization." (the slide changes to shown Aizen at a Japan First rally in 1999. )

"Everything changed in 2000 with Second Impact and more importantly the Second Russo-Japanese war triggered over both countries claim to the Kuril islands. Things came to a head on September 18, 2000 when the Russian launched a failed invasion of Sapporo, Hokkaido under Field Marshal Alexei Stovich which failed when the Russians were pinned down and forced to surrender the next day in what was deemed 'the Russian Bay of pigs' (slide changes to show Russian soldiers with hands in the air and they march pass JSDF forces). The next day on September 20, 2000 (A:N:my eighth birthday and that's no joke) as both Emperor Heisei (known in the West as Emperor Akihito) and Prime Minister Junichiro Koizumi (both real) were visiting the troops in Sapporo when Russian Field Marshal Sergei Tutov used an old Cold War nuke to destroy Tokyo-1 (changes slide to show the ruins of Tokyo-1) for which he was executed as a traitor for acting with out orders."

"We can only somewhat grateful secessionists in Chechnya decided to rebel again and even though they was suppressed, Japan survived." chimed in Fuyutsuki

Commander Ikari ignored this and kept going. "Aizen was sent away by his parents after Tokyo-1 was nuked which was good on their part because during the anarchy after the nuking and that lasted until order was restored both of his parents were killed. Aizen went to Brazil to live with relatives in the Japanese community in São Paulo. It was during this time he came across the Soldados de Deus, or

Soldiers of God, under its leader and founder Pedro Gouda as the name implies is a right-wing and Traditionalist Catholic paramilitary terrorist group. (Changes slide to show members of the group in formation.) Their goal is to eradicate all forms of 'heresy' including NERV because we destroy the Angels who they see as the messenger's of God."

"It is important to note both Pope John Paul II and Pope Benedict XVI, the Vatican, The Archbishop of São Paulo who is the head of the Catholic church in Brazil, the mainstream Catholic church and the overwhelming majority of Catholics have denounced this group." added Fuyutsuki

Commander Ikari again ignored the distraction and continued. "Shortly after Aizen arrived in Japan the Franco-Brazilian war broke out (changes slide to show Brazilian tanks in Cayenne which is the capital of French Guiana) This of course was because while France struggled to stay together a group of generals in the Brazilian army annexed French Guiana as a state of Brazil. Once the French re-established order they went to war with Brazil to regain this territory (changes slide to show a French war ship of the coast of Belém,Brazil). The French failed on most landings, but did manage to occupy Rio de Janeiro (changes slide to show French soldiers celebrating with the statue of Christ the redeemer in the background).

The the French smuggled agents into São Paulo and after contacting secessionists established the Republic of São Paulo, which was a French puppet state. At first it was liberal country, but then the Soldiers of God staged a coup and took over (changes slide to show members of the Soldiers of God celebrating after the successful coup. Aizen is dead center holding the São Paulo flag which is composed of thirteen horizontal black and white stripes and has a red canton with a blue silhouette of Brazil in a white circle and four yellow five-pointed stars appear in the each corner of the canton) and they replaced the former government by establishing the State of São Paulo which was no longer a puppet state but now an independent and theological fascist dictatorship even going so far as to revive the Inquisition.

However the Brazilian government regained control from the militarists and decided to end the war with everything to back to before. As a sign of good will the French even helped the Brazilians crush the new government in São Paulo (changes slide to show Brazilian flag again waving over São Paulo).

Punishment for anyone who led the takeover or invasion but especially in the São Paulo secession attempt were arrested, tried and executed including Gouda. As a result many fled including Aizen who returned to Japan living where he educated himself and helped to revive the Soldiers of God (changes slide to show foundation ceremony for the revival of the Soldiers of God with Aizen dead center) in Japan in 2002. He was ranked Lieutenant and reached Captain in 2005.

The issue was the leader, Ganju Hayama (changes slide to show Hayama) the first cousin of Gouda and now leader. Hayama was a moderate who wanted to disarm the group and make it mainstream which made radicals like Aizen irate, and in 2003 Aizen began to secretly rearm and train the group. He also made friends with high-ranking members so he isolated Hayama. In 2007 at the fifth party celebrating the Soldiers revival in Japan, Captain Aizen and his supports launched a coup and took over (changes slide to show Aizen after the coup as the new leader).

Aizen returned the group to its roots as a terrorist organization but kept ties to legitimate groups like Japan First and the Japanese National Socialist workers and welfare party which is Neo-Nazi in nature (I kid you not there is a Neo-Nazi political party in Japan). Ever since its founding Aizen has been against NERV and in fact in 2013 he held a rally against NERV in Tokyo-2. Mr. Kiamora was present and we believe followers of Aizen took advantage of his weakened state to brainwash him. He confessed he used his master-key to get access to the apartment of Major Katsuragi so he could harm her and the pilots. He also confessed to being the one who called the Major while disguising his voice and confessed to being the person who tried to poison both Rei and Dr. Akagi as well." finished Commander Ikari.

With that the show ended, Fuyutsuki shut off the projector and turned on the light as everyone except the Commander and Sub-Commander stretched.

Doctor Akagi then cleared her throat " I have an update on Shinji" she began, but was mobbed by Misato who only backed off on the order of the Commander. "It's not good" started the doctor "I'm afraid Shinji has developed symptoms of advanced Brugmansia poisoning, due to the extended poisoning. His condition has gotten clearly worse, but Maya is watching him and since she hasn't contacted me then he is not doing any worse as of now."

Upon that everyone took their leave, both Commander Ikari and Sub-Commander Fuyutsuki went to the Commander's office.

"Professor" began Gendo "Your interruptions during the presentation were not warranted nor were appreciated at all."

"I was attempting to interject as much information as possible. Why do seem to care so much about Shinji now? You've always been so cold to him since he arrived in Tokyo-3." asked the older man.

"Exactly why. I've hurt that boy so much I can't let others hurt him. Besides I know Yui would want the people who hurt him punished."

"Dammit!" Misato cursed. While Misato and the other knew what they were dealing with, she was upset with finding out Shinji had taken a turn for the worse.

 

After the meeting she went around shadier parts of Tokyo-3 trying to find out where the Soldiers of God were but she had come up empty. From empty warehouses to bars, she was leaving her latest stop, a heroin den, She found drug addict but nothing to do with the Soldiers of God. As she left, she again failed to notice the same white van from outside her apartment.

As the two men inside nodded the sadistic passenger quickly hoped in the back, grabbed a Uzi, threw open the door, aimed where Misato was and started to fire.

**Notes for the Chapter:**

> A/N: Cliffhanger! I hope the ending made up for everything else but it was necessary. Again I don't mean to offend anyone so if you were I'm sorry but I wanted to make clear I'm not generalizing anyone which is why I had the general who nuked Tokyo-1 executed as a traitor and I added that the Soldiers of God were denounced by the Catholic church and Catholics in general (I was Catholic until 9 years old) and again it does not represent the kind, tolerant and peace-loving Catholic community as a whole just as Al-Qaeda doesn't represent the tolerant, peace and freedom Muslim community nor did Osama Bin Laden before we blew his brains out. The name Gouda was a reference to Ghost in the shell 2nd G.I.G. and if you can't tell I am really political hence why I added those conflicts. The names Aizen and Ganju as well as the rank Aizen held which was Captain are references to Bleach his former rank . Junichiro Aizen will definitely appear again but I am not sure about the other Ganju and his surname of Hayama is a reference to Kodocha. I just wanted to say about the intensive interrogation is I don't condone torture per say but I do support tactics such as water boarding only as a last resource or if it can save hundreds or thousands from being hurt. Thanks for reading and see what happened next. Please review!


	5. Chapter 5

**Summary for the Chapter:**

> Misato survives the attack, Rei and Asuka have a talk, and Misato visits Shinji then finds trouble.

**Notes for the Chapter:**

> A/N: Thanks for all the positivity for the first four chapters. I'm sorry for the length and dullness of the last chapter and and I promise I will also cut down parentheses and ramblings in my author's notes. Unfortunately this will be somewhat of a filler however it will set up the finale.

Thanks to my pre-reader gunman who also helped me with the Misato and Shinji scene

Disclaimer: I don't own Evangelion it is the property of Gainax

As the white van fled away from the scene people came out of hiding. One of these was Misato Katsuragi who had avoided being gunned down. Misato was lucky for her military training because as soon as the door slammed open her instinct to decide if it was a threat that came from training allowed her to see the Uzi and take cover before the shooting behind a mailbox as the area as a spray of bullets covered the area..

"Cowardly bastards!" the major screamed at the van. "That David Koresh wannabe can't even do his own dirty work." she mumbled to herself

She was tempted to start shooting at it but not wanting to hurt or kill someone innocent she fought the urge. Eventually the police came and conducted their report bringing people into questioning, including Misato who tried in vain to use her NERV ID to get out of this and by the time she went home it was almost 10 pm.

"Finally!" the purple haired woman called as she reached her apartment. She got out of her car and went to her apartment, "I'm home" called the tired Major as she entered the apartment.

"Hello" both Asuka and Rei called together causing Asuka to give Rei a death stare. The blunnette ignored the German and turned to Misato.

"Did you find any valuable information during interrogation?" Rei asked

Misato gave the girls an overview of the interview/interrogation while feeding Pen-Pen who had been ignored by the girls.

"So the one responsible is some crazed religious/terrorist leader with a grudge against NERV.'" said Misato who plopped down on the couch and turned on the TV.

The brunette twenty year old was talking about a breaking murder at a abandoned meat packing warehouse and she handed things over to her forty year old co-worker on the scene.

("That's right. Police discovered this grizzly murder just an hour ago and now we're getting details. The victim's name is Takumi Kiamora. Mr. Kiamora had both arms severed at the shoulder and both legs severed at the hip. He also had a large hook jammed into his chest and was hung from the ceiling. Police believe he died of blood loss because of this so who ever killed him wanted him to die slowly. The odd thing backing up this belief is a message written on the wall in what appears to be the victim's blood that reads "TO THE PURPLE HAIRED WHORE. YOU GOT THIS TRAITOR TO TALK AND THAT'S WHY HE'S DEAD. YOU ALSO SURVIVED OUR SHOOTING BUT YOU WON'T BE SO LUCKY NEXT TIME! LONG LIVE LORD AIZEN!" Police have no leads.)

"Talk about incompetence! I was at the police station for two hours." grumbled Misato who said clearly "I'm the one their talking about so we better be careful and I'll get Section 2 to add more security."

But when she reached for her cellphone it was gone and she realized she left it at NERV. Since telephone lines were still down from the last Angel battle she couldn't call anyone, Asuka was out of minutes and Commander Ikari wouldn't let Rei have a cellphone the Major left to retrieve her cellphone from NERV in case of emergency. She didn't like the ideas of leaving the girls alone but she needed that lifeline so she had to trust Section 2 who hadn't always proven themselves effective.

"Now don't open the door for anyone but me or NERV personnel you know." Misato said before leaving the apartment and closing the door shut.

"Well that should be easy. We only know a handful of people in that hollowed-out basement." groaned Asuka in exasperation

With Misato gone both Rei and Asuka were left alone much to the dismay of the redhead.

"I'm bored! Anything you want to do Wondergirl?" Asuka asked, showing desperation by asking Rei for any companionship.

"No." stated the blue haired girl in usual plain manner.

"You're so boring!" Asuka exclaimed, never ceasing to be amazed at the mannerism of Rei Ayanami.

"I am as interesting as ordered by Commander Ikari." came the simply response from Rei.

"There you go again! Always with 'Commander Ikari' this and 'Commander Ikari' it's so annoying! You're just the Commander's doll! Is there anyone else you care about?" exclaimed the Second child.

"Shinji!" Rei snapped back followed by several minutes of awkward silence.

"I'm sorry for losing my temper at-" Rei began, but was interrupted by Asuka

"You used the idiot's first name." said Asuka, completely amazed

"Yes." began Rei "Before Shinji arrived I was very obedient to the Commander. And while I still wish to serve my duty as a pilot, Shinji awoken something in me. I feel things I've never felt before. I have concern for Shinji not as a pilot, but as a person."

Asuka lowered her head "I know what you me, that boy deserves better and even though he has flaws he has been closer to me then anyone else I've known, even my own family. I know I act act like a bitch at times but-" Asuka looks up directly at Rei "Most of the time I don't mean it. Shinji and Misato have treated me nicer than I ever deserve and I just belittle them both because I just can't show people kindness. That includes you Wonder- Rei."

Rei blinked, "You used my proper first name Pilot Soryu."

"Yeah, Rei is your first name." said Asuka who then added "I'm sorry for how I treated you."

Rei smiled and said "You are forgiven, Asuka."

Both girls smiled and then turned in for bed, Asuka was glad Misato wasn't there to tease them.

 

After finding her cellphone buried under a mountain of paperwork on her desk, the purple-haired Major was about to head home,when she found herself automatically walking through the hospital wing of NERV.

She kept walking until she came to a familiar door-Shinji's.

Misato cursed herself for not visiting more often. But in her mind she could be more useful by trying out who poisoned Shinji, not just hanging around waiting to see what the doctor's had come up with to save his life.

Turning the handle and pushing the door open, Misato walked into the room and paused. Lying on the bed, tubes in his nose and needles in his arms, was her first ward. The soft beeping machine next to his bed was not enough to wake him, nor the young Lieutenant that was slumped over in the chair next to his bed.

Maya's going to be sore in the morning. Misato thought with a grin

Walking over to her, she pushed on the young woman's shoulders, rousting her

"Wa-Ha! Oh! Major I'm...I'm sorry I..." Maya stuttered

"It's alright, Maya. I won't tell. How's Shinji?" she asked

"Oh. Uh...the antidote Dr. Akagi administered to him has neutralized the majority of the poison, but there was enough lingering traces to...well, he hasn't woken up yet. I'm sorry." Maya said, grabbing her clipboard from the ground and going over her notes.

"I understand. Why don't you go get some coffee? I'll stay with Shinji for now." Misato offered

"Really? Okay. I could use some." Maya said as she lazily got up walked out of the room, a small limp in her walk as her muscles still hadn't woken up completely.

Pulling the chair over to the bed, Misato sat down, her hand reaching out and taking Shinji's hand.

"I'm sorry I haven't been by to visit you Shinji. I'm not a doctor so there isn't much I can do for you now. Sad excuses, I know, but...we've been making some headway in the case. We found the guy who poisoned you, and now we have to go after his boss. I guess something like this should have been counted on. I mean, we fight 'Angles', so it's no wonder a bunch of religious zealots want us gone. Too bad they don't know the these Angels have nothing to do with the Bible. But trying to convince other people who have their own way of thinking...it's like trying to to dig a tunnel through a mountain with a rubber mallet." she said with a laugh. "Rei has moved in with us, for her own safety. You'd be surprised little her and Rei actual fight. And I know Asuka won't admit it but she misses you. I do too. You made that dreary little apartment a real home, Shinji. Before it was just me and Pen-Pen, and then you came along, and then Asuka." she said, tears falling from her eyes and landing on Shinji's bed. "You're not dead, Shinji, so please...please come back to us. We all need you. I need you. I never told you this before, but...you're like the son I never had. So please, Shinji, get better and come home. I'll find the people who did this to you, but please...give me something to look forward to."

Misato's ears cocked to the left, hearing Maya's footsteps coming down the hallway.

"I'll be back to see you again. I promise." Misato said as she got up and bending over planted a kiss on his forehead.

She stood up as Maya entered the room, two cups of coffee in her hands.

"Coffee, Major?" Maya asked

"I'd better not. I really need to get some sleep." Misato said as she turned and headed for the door. "I'll be back tomorrow. Good night, Maya."

"Good night, Major." said the young Lieutenant as said Misato walked out of the door slowly.

As she drove on the empty streets she fought of sleep, it had been a long day and the fact it was nearly midnight didn't help.

As Misato drove down the empty streets of Tokyo-3 she fought the sleepiness that was trying to over take her. She pondered the idiocy at refusing Maya's coffee. It probably would have been enough to get her home.

As she drove down Tokugawa street a man staggered in front of the car. He was bruised and shirt ripped and splattered with blood.

Misato stopped her car and got out to help the man who she could now tell was in his mid-thirties.

"Who did this?" she asked expecting him to answer thugs or at worst yakuza but instead his answer shocked Misato

"A terrorist group called the Soldiers of God. I'm a former member who left, the found me and now they're going to kill me!"

"What?" Misato exclaimed "Where are those frigging bastards? They tried to kill my ward, my friends and me, and I want their asses!"

"Over there" the man weakly responded pointing to a slightly open door. Misato drew her gun and after quickly getting into position opened the door only to find the room empty.

"What they hell-" Misato began but was unable to finish her statement has she was struck in the back of the head, rendering her unconscious. Behind her was the man she was helping holding a lead pipe as other came out of the shadows.

"You!" he said pointing to one of the men "Call Lord Aizen and tell him we got the target."

As his subordinate followed orders the assailant added. "We will destroy NERV and then the Angles shall complete their mission of inciting Third Impact which will bring the Second Coming of Christ."

As Misato was tied up the man who tricked her went to wash the fake blood and makeup off him.

**Notes for the Chapter:**

> A/N: Another cliffhanger! In case you didn't figure it out Misato has been captured by the Soldiers of God after falling into a trap and now their agenda is revealed. I know the scene with Asuka and Rei was out of place a bit but I needed space to fill and tragedy brings people together. I'm mostly surprised because I thought I was crappy at writing mushy scenes. Anyway next chapter is the final one so keep posted and don't forget to review!


	6. Chapter 6

**Summary for the Chapter:**

> Mistao has been captured but she isn't going to let that stop her from getting justice for Shinji.

**Notes for the Chapter:**

> A/N: Well here it is the final chapter of "A Mother's Justice". By the way in case you were wondering this occurs between episodes 20 and 21. I won't go into a long rant but I want to thanks everyone who supported this story because it wouldn't be possible without you.

Thanks to my pre-reader gunman

Disclaimer: I don't own Evangelion it is the property of Gainax

Misato woke up in a daze the next morning. The last thing she remembered was finding that guy on the on the street who aid he was attacked by the Soldiers of God and-.

"It was a trap... and I fell for it." Misato softly said to herself in a very bitter tone. She looked around noticing she was in a small jail cell which was the well lite, Misato could make out the lime green wall paper on the room outside the cell.

"Someone needs to call Martha Stewart in here now." Misato thought sarcastically. Misato tired to move and noticed her body and then realized she was bound, her arms tied behind her back and ankles were tied together.

"Don't bother, your a prisoner of Lord Aizen now and he will pass judgment." a think and burly answer came from the guard left in charge of Misato from hi desk. The guard stood 6 ft 4 inches and was 250 lbs., and almost all muscle

"What happened to 'Judge not lest yet ye be judged' huh?" asked Misato banking on her vague knowledge of Christianity and thanking her job for that.

The guard grunted and ignored her, only for Misato to recognize him. He was Kento Kusakabe aka the 'Old Hakone Rapist'. From 2002 to 2005 he was responsible for a series in the Old Hakone district of Tokyo-3. He got away because police presence in Old Hakone is non-existent after night fall which is still the case now.

Misato still remembered how big it was when he was captured, Kusakabe was stopped for speeding during which time he was arrested for the possession of heroin with intent to distribute and it was at the police station where DNA was taken that connected him to the crimes. He served seven years in prion before being released and that's when Aizen most likely go to him.

Twenty minutes after she regained conscientiousness Kusakabe heard a soft sobbing coming from the cell. Looking inside he saw it was Misato and a Kusakabe was over come with overcome with lust because that was one of his favorite parts of committing the crime he did. Unlocking the cell door, Kusakabe entered the cell and stood over Misato eyes full of lust as he got ready to ravage the bound up woman.

However, the moment he got close enough, he collapsed to to the floor of the cell in pain. You see Misato discovered the binding she was in was loose and banking on the fact Kusakabe couldn't resist going back to his old ways she lured him into her trap then Misato delivered a kick to the groin dropping the man and showing why Misato was the Director of Operations at NERV.

"Once a perverted bastard, always a perverted bastard." said the major as she removed her bindings and rank over to the desk grabbing her jacked complete with cellphone and gun.

"They did a sloppy job for a supposed big terrorist group." said the purple haired woman who then went back to Kusakabe.

Misato kicked Kusakabe in the face, knocking him on his chest. Misato then drove the back of her heel into his shoulder and grabbing, his wrist began pulling his arm straight up. The force of the pulling was worsened by the the fact his shoulder was being pinned and couldn't move brought great pain to the man. It was worsened even more by the fact he Misato had heels on.

"Okay where are we, and we the fuck is Aizen?" yelled Misato

After struggling for a few moments a humiliated and pained Kusakabe gave in.

"This is the compound of the Soldiers of God, in the mountains outside Tokyo-3." he said

"Where is Aizen?" screamed a furious Misato

"The Center Hall!" yelled Kusakabe in horrid pain. "This room is below the Southern wing, go up the stairs and follow a left then right zigzag pattern and you'll find yourself there!"

Misato let go of the arm of Kusakabe then drew her gun and aimed it at his head. "This is for the women you hurt" he said and fired killing Kusakabe. "You said rapists aren't helpful?" she though after which she grabbed the gun Kusakabe had in his waist before running up the stairs.

 

Once Misato reached the top of the stairs she found in a long and winding corridor. Finding a window and is able to get a faint cellphone signal which he uses to make a call.

"Kaji? It's Katsuragi here. I'm at the compound of the Soldiers of God in the mountains here outside Tokyo-3. If I don't make it tell Asuka, Rei and Pen-Pen how much I cared for them. Thanks Ryoji." before hanging up and continuing her mission.

 

Misato ran down the hall and as he move he heard the running of footstep and knew the Soldier were onto her. Her advantage was they didn't know where she was yet..

"Hey, the prisoner escaped! Kill her!" yelled an unknown voice and Misato who saw five Soldiers members who had come around the corner and spotted her. They brought their Uzis up and fired at her. Misato saw a steel door was next to her and rushed it, ducking inside she took cover from the gunfire. A minute later the gunfire stopped and Misato quickly jumped out, firing and killed the men.

Catching a quick breath, Misato kept running she ran into another group of men this time with handguns kept firing. Misato returned fire but was shot in the side and collapsed to the ground. She shook it off and kept firing until only one was left. But as Misato went to fire she found her magazine was empty.

"I give up." she said with her head lowered and walked to the man, both hands in the air.

 

Once Misato reached him the terrorist lowered his gun with a smirk. It was in that moment Misato drew the gun she took from Kusakabe out of her jacket pocket and pulled it on the Soldier killing him.

"What a fool." she said with a grin on her face and began to run again only to be knocked down by a huge explosion that shook the compound.

"What was that!" said the purple haired woman, only to shake the worry and continue but minutes later automatic gun fire and boot running on the ground filled the compound.

 

As Misato got closer she was unexpectedly grabbed from behind as someone threw their forearm and wrapped it around her throat.

"Well look you we have here." Misato recognized the voice, it was the same person who loured her into the trap, and had also been driving the white van which had been following her.

"Looks like fresh meat." he continued "We know what do with that right?"

Misato looked and saw the same man who fired an Uzi at her outside the heroin den in front of her

and when she looked down at his right hand she saw in it a carving knife in his hand.

Misato struggled but the man took several slashes embedding the knife into Misato each time.

"I hate to end so soon." the sadistic knife wielder began, "But we have other things to do mainly killing those brats in your care and defending our compound so goodbye."

The man came in one more time to slash the jugular of Misato. But with everything she had the bleeding Misato got her leg up and kicked him in the chest sending him flying back.

"Why you little bit-" the man holding Misato began to hiss before she grabbed him by collar, and threw him over her shoulder.

The knife wielding man charged at Misato who knocked him down with a right hook and and was followed by her kicking the man who was holding her in the stomach.

"You're dead!" yelled the knife wielder who took a wild swing at Misato but his scream ruined his surprise allowing Misato to grab his knife hand and thrusting it into the right eye of the other terrorist killing him instantly.

"No! Ichiro, talk to me!" yelled out the sadistic man hoping his friend was alive but to no avail. As the man kept trying to revive his friend Misato took out her gun, and shooting him the back of the head which killed him, before continuing.

"Damn it, this really bad." groaned the purple haired maiden as she stumbled down the hall of the Soldiers of God compound. Though she escaped the carving knife did serious damage and Misato was in trouble. Misato knew ribs were broken and from the blood gushing out and possible internal injuries. She knew fell well she could bleed to death before she got Aizen but she was determined to get revenge, even is she died in the process. She pushed on.

 

Misato continued down the winding hall she was worried, she was bleeding badly, the sound of automatic gun fire filled the compound and the lack of terrorists that tried to stop her put her on edge. She also remembered what the knife wielder said "defending our compound". This confused Misato, but now wasn't the time.

"Hurry, we can't let them take over!" the voice of an unknown man echoed down the hall Misato was in, she quickly ducked into a open door. Several men ran past all wearing officer's uniforms and Misato could tell by the insignia on their uniforms they were all Generals, who unlike the others who wore paramilitary uniforms wore the high ranking officers in the Imperial Japanese Army and they were carrying handguns and had a katana on their left hip.

"We have to make sure the prisoner is still in her cell." said one of the men as they passed the door.

This confused Misato but he brushed it off and soon as they passed she jumped out from the door ambushing the last of the men, before they could react.

"Now for Aizen." said a determined Misato as she began to move however she staggered more than ran down the corridor. However, she was dizzy, lightheaded, nauseous, and felt faint, all of these were signs of blood loss. Misato knew that she was in trouble as the Major left a trail of blood behind her as she moved on.

 

"Dammit, at this point I'm might not make it to Aizen." said Katsuragi as she stumbled down the hall trying to ignore the automatic gunfire that got louder as it got closer.

 

Finally the corridor ended at a large pair of doors that led to the Central Hall and Aizen. After pushing the doors open Misato entered the room. It was a large and bare, traditional style room, wood floors, a bare ceiling, and bare walls with a light brown wallpaper on them, the wall directly across from the door which had a large portrait of former Prime Minister and convicted war criminal Hideaki Tojo. Across from the doors was a stage and a podium. A large throne which was an exact replica of the throne of the Japanese Emperor dead center on the stage, and on it wearing the uniform of a Marshal in the Imperial Japanese Army, the highest rank possible in the IJA complete with insignia and with a katana by his side was the leader, Junichiro Aizen.

"Major Misato Katsuragi." began the terrorists mastermind slyly "So we meet at last."

"You'll die for what you did to Shinji!" yelled the anger Misato

"Oh?" replied Aizen plainly before adding with disgust in his voice. "It's a shame he survived. I can't stand it when the vermin that I've ordered exterminated survive. Hell, why I let those fools live after they failed to kill you outside the heroin den is beyond me. "

"You bastard!" yelled Misato who drew the gun she had taken from Kusakabe and aimed it at Aizen who simply smiled, stood up and drew his gun from it's holster then aimed that at Misato. The room was silent except for the sound of blood dripping from Misato onto the wood floor.

After a few moments the two began shooting. The two weaved in a zig-zag pattern through out the empty room to the others gunfire until they both in the same place as they began.

"You're dead, Aizen!" yelled as she aimed but was out of ammunition. Aizen who was also out of ammunition threw gun aside, grabbed his katana and jumped off the stage close lining the unsuspecting Major while she checked her cartridge. Aizen jumped right back up with his katana in his hand.

"It's over" said Aizen coldly as he drew his katana from his sheath and walked over to Misato.

Aizen drew all hi force brought the katana straight down to the forehead of his foe but Misato drew up her hands and clasping them together caught the blade. Misato then drew Aizen in by the blade and monkey flipped him causing the terrorist leader to crash against the wall breaking the portrait of Toji in the process.

As he was through Aizen dropped his katana, Misato picked it up and charged jumping and taking a swing at Aizen who ducked and delivered a standing side kick, which knocked down Misato, and allowed Aizen to take back his katana.

"Now you die!" yelled the terrorist mastermind as he charged with his katana swinging.

Misato kept ducking but was quickly pinned against the wall.

Aizen let out a primal scream and charged but Misato, imitating the Matrix, bent backwards and delivered a punch to the stomach followed by a headbutt which sent Aizen staggering back. Misato quickly followed that with a running knee to the nose of Aizen and then an uppercut which sent Aizen crashing into the podium which exploded.

"You bitch!" yelled Aizen with blood running from his nose as he threw the throne he was pervasively sitting on at Misato who ducked. The throne hit the ground and exploded like a cheap bar stool

Misato tucked her head in and rolled on the ground avoiding serious injury, she was able to see Aizen jump off the stage and charge at her. Misato who quickly grabbed one of the legs broken off from the throne and used it as a kendo stick to combat Aizen, being ever so resourceful as she was.

The two went back and forth in an even dual, until Misato started to get woozy and feel lightheaded. Her blood lose was getting to her and Aizen took advantage as he pushed Misato back towards the wall where she would be trapped.

As a dizzy Misato was being forced back by Aizen, he took a massive swing at Misato to either kill her or at least inflict a serious injury which could cause her to bleed to death.

As Aizen swung Misato, weak from blood loss and tired from the battling, managed to get the severed throne leg she was wielding above her head and by some fortune the katana blade of Aizen got stuck.

Seeing the terrorist leader was stunned, Misato with the little energy she had left, she flipped Aizen over her head and slammed him against the wall. As he attempted to get up, Misato pounced on him and wrapped her hands around the his throat of the as she slammed him against the wall and began to choke the life out of him.

"I kill you right now, you bastard!" screamed the enraged Katsuragi as she strangled Aizen with the goal of killing him. But a voice broke her train of thought.

"Katsuragi!" Misato looked surprised to to the doorway and saw Kaji standing inside it.

"Why are you here?" asked a confused Misato, who never moved her hands from the throat of Aizen.

"The JSSDF stormed the compound and have taken it over." replied the unshaven spy

"How did they know where it was?" asked the purple haired Major who subconsciously loosened her grip on Aizen.

"When we found out you were captured Commander Ikari called up the JSSDF, and after threatening them with Unit-00, they mobilized so when we found you they could attack. When you called me, Ritsuko traced it and Commander Ikari informed the JSDFF who ordered the compound taken over and Aizen taken alive." replied the triple agent.

Luckily, the Committee knew if this group succeeded the Angels would incite Third Impact. This of course would prevent their Third Impact so the old men decided not to intervene so this common enemy could be eliminated.

Now it all made sense: the explosion, the gunfire and the statements about the compound being taken over was JSSDF. But Aizen being left alive was not going to happen.

"No way! Aizen is dead! I don't care what happens to me!" yelled Misato, hell bent on killing Aizen

"What about the kids?" asked Kaji trying to get her to reconsider.

"Rits is the legal guardian of Rei and you can look after Asuka." retorted Misato.

"You forgot someone." said Kaji causing Misato to again tighten her grip.

Seeing this Kaji pulled out his phone and using the speed dial made a call.

"Rits its me."

"Great, he's moving on quick." though Misato to herself.

("Put him on") said Kaji over the phone which he then placed to the ear of his lover.

("Misato?") came a faint voice from the other end which caused Misato to drop Aizen.

"Shinji?" said the woman in disbelief as she took the phone while tears began to roll down her cheeks.

("I'm sorry.") he said so usual for him causing an overcome Misato dropped to he knees crying.

"Its alright, sweetie, you're alive and that's what matters." responded Misato through sobs

Kaji backed away so she could be with Shinji at this moment. Aizen, seeing his chance, tried to escape but Kaji tackled him and delivered a hay maker that knocked him out cold.

"Well" said Kaji as he sparked up a cigarette "I'd say mission accomplished." before turning back with a smile looking at Misato talking to Shinji on the phone.

He then thought to himself "Though I have to admit, it was pretty ingenious of Ritsuko and the Commander to purge the last of the poison out of Shinji by putting him into Unit-01 and letting the LCL pump into his body. Wonder what made them think of that?" as he kept an sharp eye on Aizen.

He had no way to know Shinji's mother, Yui Ikari, was in Unit-01 had been responsible for purging out the rest of the poison.

Which I exactly what Gendo was counting on.

 

EPILOGUE

With the success of the raid by the JSSDF, the Soldiers of God were eliminated. Those captured were turned over to the Japanese Government and tried for domestic terrorism. They were convicted and given life in government prisons. Those killed in the raid on both sides were buried and compound demolished. Aizen was personally transported by Kaji and was said to have died from untreatable injuries received fighting Misato.

This was not true...

"Where am I?" said Aizen before averting his eyes. The brightness of the light, be it artificial. Still hurt after days in the dark isolation of the NERV detention cell.

It was only after his eyes had adjusted to the light that Aizen saw that he wasn't alone. Looking around he was surrounded by tanks full of an orange liquid and in them were multiple copies of the First Child, naked and staring at him.

Aizen had come face to face with the "Reiquarium".

"What the Hell!" yelled Aizen freaked out by what he was seeing but as he tried to escape he found him self tied down to a table.

"Hello, Mr. Aizen." came a voice from the shadows, and Aizen could see a man in a suit with a beard, orange-tinted sunglasses and white gloves in had walked in front of him.

"Gendo Ikari, the Commander of NERV." replied Aizen before asking "What does the most famous heretic in Japan plan to do with me?"

"Punishment" replied the Commander "For trying to kill my son."

"Oh, that was your kid." said the terrorist mastermind "I am sorry he lived."

Gendo just smirked as two more people joined him

"Aizen may I introduce you to Sub-Commander Kozo Fuyutsuki and the head of Project E, Dr. Ritsuko Akagi." replied the holder of Adam

"What do you plan to do with me?" asked Aizen who then saw the cart of various surgical tools and various colored liquids in various jars pushed out by the older man. Trying to see this is when Aizen realized he was tied down to an operating table.

"You see, Mr. Aizen," began Ikari "I've always had several medical procedures I wanted to test out but since they are illegal and highly dangerous I have never been able to find a human test subject. That is until now. I though the clones could use a show, being cooped up in these tanks all the time."

Panic overtook Aizen as he tried to wriggle free but Doctor Akagi injected a sedative to subdue him, though it didn't remove his ability to feel pain.

Several hours and a dozen tests that violate the UN Charter and bordered or were clear cases of crimes against humanity later, the body of the late Junichiro Aizen was buried in an unmarked grave.

"That was for you, Yui." said the Commander as he watched the body of Aizen being laid down.

 

At the Katsuragi/Ikari/Soryu residence everything was back to normal, except the extra beer stocked up from the raise Misato got.

Rei had returned to her apartment and Shinji returned home the day after the raid with a clean bill of health. Misato had received medical treatment from Dr. Akagi for her injuries and after returning home with Shinji, against the doctor's orders, she was placed on a temporary medical leave with pay to recover. Though she didn't slow down at all.

"Move over and give me the remote baka!" yelled Asuka as she forced Shinji to give in to her demands (again) but this time the girl said, "Good to have you back, idiot."

However that was sentence was said only to herself.

"Stop fighting you two." called Misato from the table going over data from the last Angel battle which she had neglected because of the recent events and downing her fifth beer.

The Major stared at Shinji and smiling said to Pen-Pen, "Everything is back the way it should be."

**Notes for the Chapter:**

> A/N: Well there it is. My first multi-chapter and serious story. I figured the Committee wouldn't care if the JSSDF took out the Soldiers of God since the group would interfere in their plans. Also, I used the JSSDF because they are the only real military force featured and besides the only other option I had was Section 2 and they would have found every was to screw up. Enjoy this portrayal of Gendo because it will likely be the only time I portray him like this. I hoped you enjoyed and thanks to everyone who supported it. Look out for my future works and don't forget to review!

**Author's Note:**

> A/N: That's chapter one of the story. This story is T for now but may change to M later for violence and language. Asuka and Rei will appear next chapter and may show up later but their roles will be small in this story. Yoshi Nohara (the surname is a a nod to Shin-Chan) and Ai (a nod to Hell girl and Briana Palencia who did a great job as Rei in the Rebuild) Matsumoto (a nod to Bleach though here she is Nohara) are mine and may appear in future stories as background characters. There will be five chapters total to this. Chapter 2, Misato begins to hunt down Shinji's would-be killer. Read and review!
> 
> "All women become like their mothers. That is their tragedy. No man does. That is their tragedy"- Oscar Wilde The importance of being Ernest (1895).That just seems like a good quote for Neon Genesis Evangelion.


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